Computational methods for analyzing genome-wide chromosome conformation capture data

Abstract Summary Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery. Availability and implementation epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.

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epiTAD: a web application for visualizing high throughput chromosome conformation capture data in the context of genetic epidemiology

10.1101/243840 ◽

2018 ◽

Author(s):

Jordan H. Creed ◽

Garrick Aden-Buie ◽

Alvaro N. Monteiro ◽

Travis A. Gerke

Keyword(s):

High Throughput ◽

Genetic Epidemiology ◽

In Silico ◽

Web Application ◽

Chromosome Conformation Capture ◽

Chromosome Conformation ◽

Web Based ◽

Genome Wide ◽

Public Data ◽

Complex Scale

AbstractThe increasing availability of public data resources coupled with advancements in genomic technology has created greater opportunities for researchers to examine the genome on a large and complex scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic structures and annotations across multiple databases and platforms in an interactive manner in order to facilitate in silico discovery. epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/.

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No kissing in the nucleus: Unbiased analysis reveals no evidence of trans chromosomal regulation of mammalian immune development

10.1101/212985 ◽

2017 ◽

Cited By ~ 3

Author(s):

Timothy M. Johanson ◽

Hannah D. Coughlan ◽

Aaron T.L. Lun ◽

Naiara G. Bediaga ◽

Gaetano Naselli ◽

...

Keyword(s):

Gene Expression ◽

Cell Fate ◽

Immune Cells ◽

Chromosome Conformation Capture ◽

Chromosome Conformation ◽

Immune Development ◽

Regulate Gene Expression ◽

Genome Wide ◽

Capture Technique ◽

Regulate Gene

SummaryIt has been proposed that interactions between mammalian chromosomes, or transchromosomal interactions (also known as kissing chromosomes), regulate gene expression and cell fate determination. Here we aimed to identify novel transchromosomal interactions in immune cells by high-resolution genome-wide chromosome conformation capture. Although we readily identified stable interactions in cis, and also between centromeres and telomeres on different chromosomes, surprisingly we identified no gene regulatory transchromosomal interactions in either mouse or human cells, including previously described interactions. We suggest that advances in the chromosome conformation capture technique and the unbiased nature of this approach allow more reliable capture of interactions between chromosomes than previous methods. Overall our findings suggest that stable transchromosomal interactions that regulate gene expression are not present in mammalian immune cells and that lineage identity is governed by cis, not trans chromosomal interactions.

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A statistical model of intra-chromosome contact maps

Soft Matter ◽

10.1039/c4sm02519a ◽

2015 ◽

Vol 11 (5) ◽

pp. 1019-1025 ◽

Cited By ~ 20

Author(s):

Leonid I. Nazarov ◽

Mikhail V. Tamm ◽

Vladik A. Avetisov ◽

Sergei K. Nechaev

Keyword(s):

Fine Structure ◽

Statistical Model ◽

Chromosome Conformation Capture ◽

Chromosome Conformation ◽

Contact Maps ◽

Genome Wide ◽

A Genome ◽

Capture Method ◽

Chromosome Maps

A statistical model describing a fine structure of the intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi–C) is proposed.

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Faculty Opinions recommendation of Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1033299.375238 ◽

2006 ◽

Author(s):

Wendy Bickmore

Keyword(s):

Es Cells ◽

Chromosome Conformation Capture ◽

Chromosome Conformation ◽

Mouse Es Cells ◽

Genome Wide

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Targeted high-resolution chromosome conformation capture at genome-wide scale

10.1101/2020.03.02.953745 ◽

2020 ◽

Cited By ~ 1

Author(s):

Damien J. Downes ◽

Matthew E. Gosden ◽

Jelena Telenius ◽

Stephanie J. Carpenter ◽

Lea Nussbaum ◽

...

Keyword(s):

High Resolution ◽

Fold Increase ◽

Chromosome Conformation Capture ◽

New Method ◽

Entire Genome ◽

Chromosome Conformation ◽

Target Sequencing ◽

Genome Wide ◽

Technical Modifications ◽

Wide Scale

ABSTRACTChromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a >3-fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.

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